Four families of folate-independent methionine synthases

Autoři: Morgan N. Price aff001;  Adam M. Deutschbauer aff001;  Adam P. Arkin aff001
Působiště autorů: Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, Berkeley, California, United States of America aff001;  Department of Bioengineering, University of California, Berkeley, California, United States of America aff002
Vyšlo v časopise: Four families of folate-independent methionine synthases. PLoS Genet 17(2): e1009342. doi:10.1371/journal.pgen.1009342
Kategorie: Research Article


Although most organisms synthesize methionine from homocysteine and methyl folates, some have “core” methionine synthases that lack folate-binding domains and use other methyl donors. In vitro, the characterized core synthases use methylcobalamin as a methyl donor, but in vivo, they probably rely on corrinoid (vitamin B12-binding) proteins. We identified four families of core methionine synthases that are distantly related to each other (under 30% pairwise amino acid identity). From the characterized enzymes, we identified the families MesA, which is found in methanogens, and MesB, which is found in anaerobic bacteria and archaea with the Wood-Ljungdahl pathway. A third uncharacterized family, MesC, is found in anaerobic archaea that have the Wood-Ljungdahl pathway and lack known forms of methionine synthase. We predict that most members of the MesB and MesC families accept methyl groups from the iron-sulfur corrinoid protein of that pathway. The fourth family, MesD, is found only in aerobic bacteria. Using transposon mutants and complementation, we show that MesD does not require 5-methyltetrahydrofolate or cobalamin. Instead, MesD requires an uncharacterized protein family (DUF1852) and oxygen for activity.

Klíčová slova:

Archaea – Cobalamins – Genomics – Methanogens – Methionine – Phylogenetic analysis – Protein domains – Proteomes


1. Goulding CW, Postigo D, Matthews RG. Cobalamin-dependent methionine synthase is a modular protein with distinct regions for binding homocysteine, methyltetrahydrofolate, cobalamin, and adenosylmethionine. Biochemistry. 1997 Jul 1;36(26):8082–91. doi: 10.1021/bi9705164 9201956

2. González JC, Peariso K, Penner-Hahn JE, Matthews RG. Cobalamin-independent methionine synthase from Escherichia coli: a zinc metalloenzyme. Biochemistry. 1996 Sep 24;35(38):12228–34. doi: 10.1021/bi9615452 8823155

3. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2010 Jan;38(Database issue):D473–9. doi: 10.1093/nar/gkp875 19850718

4. Deobald D, Hanna R, Shahryari S, Layer G, Adrian L. Identification and characterization of a bacterial core methionine synthase. Sci Rep. 2020 Feb 7;10(1):2100. doi: 10.1038/s41598-020-58873-z 32034217

5. Pejchal R, Ludwig ML. Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication. PLoS Biol. 2005 Feb;3(2):e31. doi: 10.1371/journal.pbio.0030031 15630480

6. Schröder I, Thauer RK. Methylcobalamin:homocysteine methyltransferase from Methanobacterium thermoautotrophicum. Identification as the metE gene product. Eur J Biochem. 1999 Aug;263(3):789–96. doi: 10.1046/j.1432-1327.1999.00559.x 10469143

7. Matthews RG, Smith AE, Zhou ZS, Taurog RE, Bandarian V, Evans JC, et al. Cobalamin-Dependent and Cobalamin-Independent Methionine Synthases: Are There Two Solutions to the Same Chemical Problem? Helv Chim Acta. 2003 Dec;86(12):3939–54.

8. de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A, Cruaud C, et al. A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol. 2008 Mar 4;4:174. doi: 10.1038/msb.2008.10 18319726

9. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014 Jan;42(Database issue):D222–30. doi: 10.1093/nar/gkt1223 24288371

10. Price MN, Deutschbauer AM, Arkin AP. Gapmind: automated annotation of amino acid biosynthesis. mSystems. 2020 Jun 23;5(3). doi: 10.1128/mSystems.00291-20 32576650

11. Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, et al. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PLoS Genet. 2018 Jan 11;14(1):e1007147. doi: 10.1371/journal.pgen.1007147 29324779

12. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003 11;4:41. doi: 10.1186/1471-2105-4-41 12969510

13. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–402. doi: 10.1093/nar/25.17.3389 9254694

14. Menon AL, Poole FL, Cvetkovic A, Trauger SA, Kalisiak E, Scott JW, et al. Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome. Mol Cell Proteomics. 2009 Apr;8(4):735–51. doi: 10.1074/mcp.M800246-MCP200 19043064

15. de Crécy-Lagard V, Phillips G, Grochowski LL, El Yacoubi B, Jenney F, Adams MWW, et al. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate. ACS Chem Biol. 2012 Nov 16;7(11):1807–16. doi: 10.1021/cb300342u 22931285

16. UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019 Jan 8;47(D1):D506–15. doi: 10.1093/nar/gky1049 30395287

17. Basu MK, Selengut JD, Haft DH. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC Bioinformatics. 2011 Nov 9;12:434. doi: 10.1186/1471-2105-12-434 22070167

18. Radle MI, Miller DV, Laremore TN, Booker SJ. Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. J Biol Chem. 2019 Aug 2;294(31):11712–25. doi: 10.1074/jbc.RA119.007609 31113866

19. Harms U, Thauer RK. The corrinoid-containing 23-kDa subunit MtrA of the energy-conserving N5-methyltetrahydromethanopterin:coenzyme M methyltransferase complex from Methanobacterium thermoautotrophicum. EPR spectroscopic evidence for a histidine residue as a cobalt ligand of the cobamide. Eur J Biochem. 1996 Oct 1;241(1):149–54. doi: 10.1111/j.1432-1033.1996.0149t.x 8898900

20. Zhuang W-Q, Yi S, Bill M, Brisson VL, Feng X, Men Y, et al. Incomplete Wood-Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi. Proc Natl Acad Sci USA. 2014 Apr 29;111(17):6419–24. doi: 10.1073/pnas.1321542111 24733917

21. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, et al. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010 Jan;38(Database issue):D396–400. doi: 10.1093/nar/gkp919 19906701

22. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004 Mar 19;32(5):1792–7. doi: 10.1093/nar/gkh340 15034147

23. Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490 20224823

24. Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, et al. Metabolic traits of an uncultured archaeal lineage—MSBL1—from brine pools of the Red Sea. Sci Rep. 2016 Jan 13;6:19181. doi: 10.1038/srep19181 26758088

25. Fu H, Metcalf WW. Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species. J Bacteriol. 2015 Apr;197(8):1515–24. doi: 10.1128/JB.02605-14 25691524

26. Borrel G, Adam PS, Gribaldo S. Methanogenesis and the Wood-Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association. Genome Biol Evol. 2016 Jun 13;8(6):1706–11. doi: 10.1093/gbe/evw114 27189979

27. Sorokin DY, Merkel AY, Abbas B, Makarova KS, Rijpstra WIC, Koenen M, et al. Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov.

28. Buchenau B, Thauer RK. Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid. Arch Microbiol. 2004 182(4):313–25. doi: 10.1007/s00203-004-0714-0 15349715

29. Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016 Sep 16;353(6305):1272–7.Int J Syst Evol Microbiol. 2018 68(7):2199–2208. doi: 10.1126/science.aaf4507 27634532

30. Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Res. 2019 May 21;47(9):4442–8. doi: 10.1093/nar/gkz246 31081040

31. Taurog RE, Matthews RG. Activation of methyltetrahydrofolate by cobalamin-independent methionine synthase. Biochemistry. 2006 Apr 25;45(16):5092–102. doi: 10.1021/bi060052m 16618098

32. Laitaoja M, Valjakka J, Jänis J. Zinc coordination spheres in protein structures. Inorg Chem. 2013 Oct 7;52(19):10983–91. doi: 10.1021/ic401072d 24059258

33. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004 Jun;14(6):1188–90. doi: 10.1101/gr.849004 15173120

34. Ferrer J-L, Ravanel S, Robert M, Dumas R. Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate. J Biol Chem. 2004 Oct 22;279(43):44235–8. doi: 10.1074/jbc.C400325200 15326182

35. Durot M, Le Fèvre F, de Berardinis V, Kreimeyer A, Vallenet D, Combe C, et al. Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data. BMC Syst Biol. 2008 Oct 7;2:85. doi: 10.1186/1752-0509-2-85 18840283

36. Strong LC, Rosendahl C, Johnson G, Sadowsky MJ, Wackett LP. Arthrobacter aurescens TC1 metabolizes diverse s-triazine ring compounds. Appl Environ Microbiol. 2002 Dec;68(12):5973–80. doi: 10.1128/aem.68.12.5973-5980.2002 12450818

37. Sajjaphan K, Shapir N, Wackett LP, Palmer M, Blackmon B, Tomkins J, et al. Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Appl Environ Microbiol. 2004 Jul;70(7):4402–7. doi: 10.1128/AEM.70.7.4402-4407.2004 15240330

38. Shelton AN, Seth EC, Mok KC, Han AW, Jackson SN, Haft DR, et al. Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. ISME J. 2019;13(3):789–804. doi: 10.1038/s41396-018-0304-9 30429574

39. Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, et al. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature. 2018 May 16;557(7706):503–9. doi: 10.1038/s41586-018-0124-0 29769716

40. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006 Feb 21;2:2006.0008. doi: 10.1038/msb4100050 16738554

41. Sonnhammer EL, von Heijne G, Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 1998;6:175–82. 9783223

42. Price MN, Arkin AP. PaperBLAST: Text Mining Papers for Information about Homologs. mSystems. 2017 Aug 15;2(4). doi: 10.1128/mSystems.00039-17 28845458

43. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. Tigrfams and genome properties in 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D387–95. doi: 10.1093/nar/gks1234 23197656

44. Huang S, Romanchuk G, Pattridge K, Lesley SA, Wilson IA, Matthews RG, et al. Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269. Protein Sci. 2007 Aug 1;16(8):1588–95. doi: 10.1110/ps.072936307 17656578

45. Sah S, Lahry K, Talwar C, Singh S, Varshney U. Monomeric NADH-Oxidizing Methylenetetrahydrofolate Reductases from Mycobacterium smegmatis Lack Flavin Coenzyme. J Bacteriol. 2020 May 27;202(12). doi: 10.1128/JB.00709-19 32253341

46. Price MN, Arkin AP. Curated BLAST for genomes. mSystems. 2019 Apr;4(2). doi: 10.1128/mSystems.00072-19 30944879

47. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000 Apr;17(4):540–52. doi: 10.1093/oxfordjournals.molbev.a026334 10742046

48. Laskowski RA, Swindells MB. LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model. 2011 Oct 24;51(10):2778–86. doi: 10.1021/ci200227u 21919503

49. Rozewicki J, Li S, Amada KM, Standley DM, Katoh K. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res. 2019 Jul 2;47(W1):W5–10. doi: 10.1093/nar/gkz342 31062021

50. Wetmore KM, Price MN, Waters RJ, Lamson JS, He J, Hoover CA, et al. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio. 2015 May 12;6(3):e00306–15. doi: 10.1128/mBio.00306-15 25968644

51. Lee TS, Krupa RA, Zhang F, Hajimorad M, Holtz WJ, Prasad N, et al. BglBrick vectors and datasheets: A synthetic biology platform for gene expression. J Biol Eng. 2011 Sep 20;5:12. doi: 10.1186/1754-1611-5-12 21933410

Článek vyšel v časopise

PLOS Genetics

2021 Číslo 2
Nejčtenější tento týden
Nejčtenější v tomto čísle

Zvyšte si kvalifikaci online z pohodlí domova

Hypertenze a hypercholesterolémie – synergický efekt léčby
nový kurz
Autoři: prof. MUDr. Hana Rosolová, DrSc.

Multidisciplinární zkušenosti u pacientů s diabetem
Autoři: Prof. MUDr. Martin Haluzík, DrSc., prof. MUDr. Vojtěch Melenovský, CSc., prof. MUDr. Vladimír Tesař, DrSc.

Úloha kombinovaných preparátů v léčbě arteriální hypertenze
Autoři: prof. MUDr. Martin Haluzík, DrSc.

Autoři: MUDr. Ladislav Korábek, CSc., MBA

Terapie roztroušené sklerózy v kostce
Autoři: MUDr. Dominika Šťastná, Ph.D.

Všechny kurzy
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.


Nemáte účet?  Registrujte se